Dr. Huggins is thrilled that Tiny, the space exploring robot has returned from the exploration mission to Titan. He's been working on recreating the atmosphere that exists on Titan and is excited to see the samples that were collected on the mission in the hopes of adding to his biosphere. After Allison's security breach Warren Hughes, an auditor, has come to Eureka to evaluate the relationship between Allison and Carter. Right as Tiny lands back on earth, an explosion blows off all her limbs. Carter learns that there's a large sinkhole on Titan which is being caused by methane. This is causing the ground to erode. The samples that Tiny had collected from Titan were a bit too big and now Eureka is at risk of sinking into the ground.
It seems that everyone in town is lovesick and Carter and Allison are stressing under the watching eye of Warren Hughes. Henry thinks that anything he does will never be good enough for Grace since she knew his alternate self for longer than he's known her. Zane now has a clean record and is free to leave Eureka if he wants to. Jo can only express he emotions through physical means. Fargo and Holly are mad for each other and while Holly just wants to hook up, Fargo doesn't want to miss out on really getting to know her.
After further investigation, Henry and Grace discover that the toxic gas was actually coming from somewhere in Eureka, not from Tiny. While Jo and Grace are in the greenhouse, a toxic fog knocks them unconscious. The genetically modified plants grew at lightning speed and began to absorb the toxic gasses and the girls come to. It turns out that Huggins has been removing the gasses from his biosphere and dumping them into the overloaded sewer system. The town is doomed unless someone is able to put on a space suit that's use for Titan explorations and push all the gasses into the greenhouse. Holly and Fargo step up to the plate and push their issues aside in order to save the town. After the situation is resolved the pair agrees to let the relationship take its course at its own pace. Jo throws Grace and Henry a simple wedding, exactly as they wanted. Carter and Allison eventually earn the approval of the auditor but Warren Hughes informs them that the fact that they care so much for each other is actually a liability. He tells them they must either end the relationship or resign from their job.